Bioinformatický seminár

Tue 1 Mar. 2011, 17:20

Title: Biegert and Soding. Sequence context-specific profiles for homology searching
Speaker: Laci Rampášek

Sequence alignment and database searching are essential tools in biology
because a protein's function can often be inferred from homologous
proteins. Standard sequence comparison methods use substitution matrices
to find the alignment with the best sum of similarity scores between
aligned residues. These similarity scores do not take the local sequence
context into account. Here, we present an approach that derives
context-specific amino acid similarities from short windows centered on
each query sequence residue. Our results demonstrate that the sequence
context contains much more information about the expected mutations than
just the residue itself. By employing our context-specific similarities
(CS-BLAST) in combination with NCBI BLAST, we increase the sensitivity
more than 2-fold on a difficult benchmark set, without loss of speed.
Alignment quality is likewise improved significantly. Furthermore, we
demonstrate considerable improvements when applying this paradigm to
sequence profiles: Two iterations of CSI-BLAST, our context-specific
version of PSI-BLAST, are more sensitive than 5 iterations of PSI-BLAST.
The paradigm for biological sequence comparison presented here is very
general. It can replace substitution matrices in sequence- and
profile-based alignment and search methods for both protein and nucleotide